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Conserved upstream open reading frames in higher plants.

Tran MK, Schultz CJ, Baumann U - BMC Genomics (2008)

Bottom Line: Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency.In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci.We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important.

View Article: PubMed Central - HTML - PubMed

Affiliation: Australian Centre for Plant Functional Genomics PMB 1 Glen Osmond SA 5064, Australia. michael.tran@acpfg.com.au

ABSTRACT

Background: Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency. In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci. It is unclear how prevalent conserved uORFs are in closely related plants.

Results: We used a homology-based approach to identify conserved uORFs in five cereals (monocots) that could potentially regulate translation. Our approach used a modified reciprocal best hit method to identify putative orthologous sequences that were then analysed by a comparative R-nomics program called uORFSCAN to find conserved uORFs.

Conclusion: This research identified new genes that may be controlled at the level of translation by conserved uORFs. We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important.

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Tran_Figure2.eps. 'The position of conserved uORFs within their 5'-UTRs'. It contains rice uORFs conserved in four other cereals and in Arabidopsis.
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Figure 2: Tran_Figure2.eps. 'The position of conserved uORFs within their 5'-UTRs'. It contains rice uORFs conserved in four other cereals and in Arabidopsis.

Mentions: Studies have shown that the position of an uORF within its 5'-UTR, which determines the pre-orf and intercistronic distances, can have profound effects on its function [18,22]. When we examined the positions of cereal uORFs within their 5'-UTRs we found that there was no positional preference with the exception that they were not positioned too closely to the start of their individual 5'-UTR and coding region (Figure 2). For example, all of the uORFs conserved in five orthologous cereals (5/5 result set) and in Arabidopsis were at least positioned 20 nucleotides from the start of their 5'-UTR, which is thought to be the minimum number of nucleotides required for a functional uORF [18]. We noticed that the intercistronic distances for these uORFs were generally shorter than the pre-orf distance. We also found seven uORFs, which included the functional small AdoMetDC uORF, that occupied greater than 20% of their individual 5'-UTR.


Conserved upstream open reading frames in higher plants.

Tran MK, Schultz CJ, Baumann U - BMC Genomics (2008)

Tran_Figure2.eps. 'The position of conserved uORFs within their 5'-UTRs'. It contains rice uORFs conserved in four other cereals and in Arabidopsis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2527020&req=5

Figure 2: Tran_Figure2.eps. 'The position of conserved uORFs within their 5'-UTRs'. It contains rice uORFs conserved in four other cereals and in Arabidopsis.
Mentions: Studies have shown that the position of an uORF within its 5'-UTR, which determines the pre-orf and intercistronic distances, can have profound effects on its function [18,22]. When we examined the positions of cereal uORFs within their 5'-UTRs we found that there was no positional preference with the exception that they were not positioned too closely to the start of their individual 5'-UTR and coding region (Figure 2). For example, all of the uORFs conserved in five orthologous cereals (5/5 result set) and in Arabidopsis were at least positioned 20 nucleotides from the start of their 5'-UTR, which is thought to be the minimum number of nucleotides required for a functional uORF [18]. We noticed that the intercistronic distances for these uORFs were generally shorter than the pre-orf distance. We also found seven uORFs, which included the functional small AdoMetDC uORF, that occupied greater than 20% of their individual 5'-UTR.

Bottom Line: Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency.In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci.We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important.

View Article: PubMed Central - HTML - PubMed

Affiliation: Australian Centre for Plant Functional Genomics PMB 1 Glen Osmond SA 5064, Australia. michael.tran@acpfg.com.au

ABSTRACT

Background: Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency. In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci. It is unclear how prevalent conserved uORFs are in closely related plants.

Results: We used a homology-based approach to identify conserved uORFs in five cereals (monocots) that could potentially regulate translation. Our approach used a modified reciprocal best hit method to identify putative orthologous sequences that were then analysed by a comparative R-nomics program called uORFSCAN to find conserved uORFs.

Conclusion: This research identified new genes that may be controlled at the level of translation by conserved uORFs. We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important.

Show MeSH